Variant report

Variant	rs4233497
Chromosome Location	chr1:45763753-45763754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45763746..45766388-chr1:45768053..45771001,2	MCF-7	breast:
2	chr1:45476319..45479273-chr1:45762744..45765021,2	MCF-7	breast:
3	chr1:45747656..45749487-chr1:45762522..45765596,3	K562	blood:
4	chr1:45476357..45485239-chr1:45761850..45773601,48	K562	blood:
5	chr1:45739847..45742419-chr1:45763606..45766458,2	K562	blood:
6	chr1:45747190..45749487-chr1:45762522..45764661,3	K562	blood:
7	chr1:45761540..45764503-chr1:45766248..45768946,2	K562	blood:
8	chr1:45761109..45763795-chr1:45769192..45770940,3	K562	blood:
9	chr1:45184599..45187885-chr1:45762943..45766358,4	K562	blood:
10	chr1:45763106..45764734-chr1:45769949..45772250,2	MCF-7	breast:
11	chr1:45284741..45287398-chr1:45762792..45766811,5	K562	blood:
12	chr1:45761061..45765465-chr1:45766442..45769712,4	MCF-7	breast:
13	chr1:45266060..45268077-chr1:45763524..45765330,2	K562	blood:
14	chr1:45476265..45486633-chr1:45761064..45774272,63	K562	blood:
15	chr1:45761163..45763441-chr1:45763531..45765423,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000126088	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000126107	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1144868	0.82[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs1226747	0.81[JPT][hapmap]
rs13374935	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs1612575	0.82[CHD][hapmap]
rs1938296	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1938301	0.81[JPT][hapmap]
rs2105458	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs2186219	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2356302	0.81[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs2997461	0.81[JPT][hapmap]
rs2997465	0.82[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs3009969	0.81[JPT][hapmap]
rs3009974	0.80[JPT][hapmap]
rs3009979	0.81[JPT][hapmap]
rs3121732	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs3121736	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3128438	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3128439	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3128440	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34134455	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs346693	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs346696	0.82[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs346717	0.81[JPT][hapmap]
rs346719	0.81[JPT][hapmap]
rs346724	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs346725	0.82[CHD][hapmap]
rs346732	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs346733	0.91[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs346736	0.81[JPT][hapmap]
rs365108	0.81[JPT][hapmap]
rs3850856	0.81[JPT][hapmap]
rs4233496	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4376776	0.94[ASN][1000 genomes]
rs4376777	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs454624	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs4603171	0.92[ASN][1000 genomes]
rs4660839	0.89[JPT][hapmap]
rs4660841	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs4660842	0.81[JPT][hapmap]
rs58579477	0.97[ASN][1000 genomes]
rs60115828	0.97[ASN][1000 genomes]
rs61789823	0.92[ASN][1000 genomes]
rs61789838	0.97[ASN][1000 genomes]
rs61789841	1.00[ASN][1000 genomes]
rs6429561	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429562	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429564	0.85[GIH][hapmap];0.81[MKK][hapmap]
rs72686440	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv3406025	chr1:45739908-45763848	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4233497	PDZK1IP1	cis	cerebellum	SCAN
rs4233497	HIVEP3	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45757800-45763800	Weak transcription	K562	blood
2	chr1:45760400-45764400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:45761800-45764400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:45762600-45768400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:45763000-45764000	Enhancers	Brain Cingulate Gyrus	brain
6	chr1:45763000-45764400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:45763000-45764600	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr1:45763000-45765400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:45763000-45766400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:45763200-45763800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:45763200-45763800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:45763200-45764000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr1:45763200-45764400	Enhancers	Brain Anterior Caudate	brain
14	chr1:45763200-45764400	Flanking Active TSS	HepG2	liver
15	chr1:45763200-45764600	Enhancers	Fetal Intestine Large	intestine
16	chr1:45763200-45764600	Enhancers	Fetal Intestine Small	intestine
17	chr1:45763200-45765400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:45763200-45766400	Enhancers	Brain Germinal Matrix	brain
19	chr1:45763200-45768400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:45763400-45763800	Enhancers	Brain Angular Gyrus	brain
21	chr1:45763400-45763800	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr1:45763400-45764200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr1:45763400-45764400	Enhancers	Liver	Liver
24	chr1:45763400-45764400	Enhancers	Brain Hippocampus Middle	brain
25	chr1:45763400-45765000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr1:45763600-45763800	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr1:45763600-45764600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr1:45763600-45764800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:45763600-45768200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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